I put my boaton the hard in Florida for about 6 months each year, during the hurricane season. This year, at my mechanic's recommendation, I pulled the exhaust hose and intake air cleaner off my Perkins 4108, then sealed the intake and exhaustports to prevent moist air from entering the engine. He says this is very important to preventing the engine from rusting out, which is apparently a problem with boats stored in humid climates.
Do any of you do this?

I don't store mine, but if i did, yes I would seal the ingress point for air into the engine as recommended. Often it's not immediate death of course, what happens is you get a light rust on your cylinder walls every year, very quickly this rust is cleaned off when you start the engine and this will lead to bore polishing, excessive blow-by, high oil temps, high oilconsumption, low compression, all the symptoms of a worn out motor, except it's not really worn out. Only cure is to remove engine and dis-assemble it and hone the cylinders, but if your going to do all of that, may as well re-build it.
Sounds like you have a smarter than average mechanic.
Ideally as Guy said, you'd fog the engine, which requires removal of the injectors to gain access to the cylinders, that and change the oil as your old oil may be acidic and no reason to led the acid etc away at your bearings for six months.Funny, a lot of people will "winterize" a $3,000 outboard, but not their $25,000 DIesel